Re: [Bioc-devel] Transfer Maintainership of GeoDiff
Hi, I’ve added Nicole. She should have maintainer access. Please change the DESCRIPTION file. Best, Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On Nov 15, 2021, at 1:59 PM, Nicole Ortogero wrote: > > Hi Bioconductor team, > > I was wondering if this maintainer update has been made in the system yet. > > Package: GeoDiff > New Maintainer: Nicole Ortogero < nortog...@nanostring.com> > Old Maintainer: Zhi Yang (see Zhi’s message below) > > Thanks, > > Nicole Ortogero, PhD > Bioinformatics Scientist II > NanoString Technologies, Inc. • nanostring.com > > > > > > > > > > From: Zhi Yang > Sent: Monday, November 8, 2021 11:08 AM > To: maintai...@bioconductor.org > Cc: Nicole Ortogero > Subject: Transfer Maintainership of GeoDiff > > Hello, > > We’d like to switch the maintainer for GeoDiff to be Nicole Ortogero > (nortog...@nanostring.com). We will soon update the description to reflect > the change. > > Zhi Yang > Biostatistician II > NanoString Technologies, Inc. • nanostring.com > > > > > ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Activate account in Bioconductor Git Credentials
Hi Yihang, You should have access now. Please activate your account at https://git.bioconductor.org/BiocCredentials/account_activation and add SSH keys. You’ll be able to push to the package. Make sure you are complaint with all the rules of contributions here, http://bioconductor.org/developers/how-to/version-numbering/ http://bioconductor.org/developers/ Best, Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On Nov 17, 2021, at 5:01 PM, Yihang Xin wrote: > > Hi Alex and Nitesh, > > I would like access to the package on git.bioconductor now. Alex, can you > grant me the permission? > > -Yihang > > -- Forwarded message - > From: Nitesh Turaga > Date: Wed, Nov 17, 2021 at 5:49 AM > Subject: Re: [Bioc-devel] Activate account in Bioconductor Git Credentials > To: Yihang Xin > Cc: Bioc-devel > > > Hi Yihang, > > You are only listed as ‘contributor’ but not the maintainer of the package > according to both the link you sent and the Bioconductor package DESCRIPTION > which is on git.bioconductor.org. > > You need to get access permissions from Alex Pico, who is the maintainer of > the package. Ideally, Alex would make the final sync from Github to > Bioconductor once all your development is done on Github. > > If you would like access to the package on git.bioconductor even now, please > let me know and cc Alex. > > Best, > > Nitesh > > Nitesh Turaga > Scientist II, Department of Data Science, > Bioconductor Core Team Member > Dana Farber Cancer Institute > > > On Nov 16, 2021, at 4:29 AM, Yihang Xin via Bioc-devel > > wrote: > > > > Hi, > > > > I am currently maintain the RCy3 package in Bioconductor, and I am trying > > to activate my account to add SSH keys. I think I have already added email > > address in the DESCRIPTION file of the package I maintain. You can find it > > here: > > https://github.com/cytoscape/RCy3/blob/dfd6fdc28c0fc88c0b0719ef28fdea51c9a18c32/DESCRIPTION#L17 > > > > But the website shows that my email address "is not associated with a > > maintainer of a Bioconductor package. Please check the spelling or contact > > bioc-devel@r-project.org for help." Could you help me to activate my > > account? > > > > Best, > > Yihang > > > > *Yihang Xin [He, Him, His]* > > Software Engineer II | Bioinformatics core > > yihang@gladstone.ucsf.edu > > Gladstone Institutes > > 1650 Owens St, San Francisco, CA 94158 > > > > [[alternative HTML version deleted]] > > > > ___ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Git recognizes me but denies access
Please activate your account flying-sh...@web.de for BiocCredentials. You should be good to go. Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On Nov 18, 2021, at 4:23 AM, Philipp A. wrote: > > My addresses are phil.ange...@gmail.com (not philipp) and flying-sh...@web.de. > > I’ll add a key as soon as I’m able to log in. > > Am Mo., 15. Nov. 2021 um 15:56 Uhr schrieb Nitesh Turaga > : > You have to activate the account at > https://git.bioconductor.org/BiocCredentials/account_activation. Set a > password and add Ssh keys. > > Once again, the email you are trying to activate is > 'philipp.ange...@gmail.com’. > > The problem seems to be non-matching key pairs. Add new SSH keys. > > Best, > > Nitesh > > > Nitesh Turaga > Scientist II, Department of Data Science, > Bioconductor Core Team Member > Dana Farber Cancer Institute > > > On Nov 15, 2021, at 9:54 AM, Nitesh Turaga wrote: > > > > Hi Philipp, > > > > The email address that is registered to BiocCredentials right now is > > 'philipp.ange...@gmail.com'. It doesn’t look like an institutional email > > address. > > > > Could you please confirm the email change to flying-sh...@web.de ?? > > > > Best, > > > > Nitesh > > > > Nitesh Turaga > > Scientist II, Department of Data Science, > > Bioconductor Core Team Member > > Dana Farber Cancer Institute > > > >> On Nov 15, 2021, at 2:36 AM, Carsten Marr > >> wrote: > >> > >> confirmed! > >> > >> > >> best, > >> c > >> > >> > >> > >>> Am 13.11.2021 um 15:56 schrieb Philipp A. : > >>> > >>> I no longer have control of this email address. > >>> > >>> Please add the one I’m writing from to the account. > >>> > >>> My supervisor (CC) from when I was at the institution can confirm that > >>> I’m the same person. > >>> > >>> Best, Phil > >>> > >>> Am Di., 9. Nov. 2021 um 16:24 Uhr schrieb Nitesh Turaga > >>> : > >>> Dear Phil, > >>> > >>> Please activate your account at > >>> https://git.bioconductor.org/BiocCredentials/account_activation. Add new > >>> SSH keys, because it’s possible you are not using the correct key-pairs. > >>> > >>> Nothing on our end seems out of place. > >>> > >>> The FAQ section from #13 onwards has other debugging options as well, > >>> https://bioconductor.org/developers/how-to/git/faq/. > >>> > >>> Best, > >>> > >>> Nitesh > >>> > >>> > >>> Nitesh Turaga > >>> Scientist II, Department of Data Science, > >>> Bioconductor Core Team Member > >>> Dana Farber Cancer Institute > >>> > On Nov 8, 2021, at 12:23 PM, Philipp A. wrote: > > Hi, > > My package (destiny) has been deprecated because Bioconductor’s LaTeX > environment keeps changing and breaking my docs. > > I‘m trying to fix it once again, but I get: > > $ git push upstream masterFATAL: W any packages/destiny p.angerer > DENIED by fallthru > > *Please note that this isn’t covered in the FAQ*: > > “p.angerer” indicates that it recognizes me, but still doesn’t allow me > to > push commits. > > Best, Phil > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > >>> > >> > >> --- > >> Carsten Marr > >> +49 89 3187 2158 > >> AIH Institute of AI for Health > >> Helmholtz Zentrum München > >> www.helmholtz-muenchen.de/aih/index.html > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> Helmholtz Zentrum München > >> Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH) > >> Ingolstädter Landstr. 1 > >> 85764 Neuherberg > >> www.helmholtz-muenchen.de > >> Aufsichtsratsvorsitzende: MinDir.in Prof. Dr. Veronika von Messling > >> Geschäftsführung: Prof. Dr. med. Dr. h.c. Matthias Tschöp, Kerstin Günther > >> Registergericht: Amtsgericht München HRB 6466 > >> USt-IdNr: DE 129521671 > >> > > > ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] EXTERNAL: LazyData: false and accessing data in the YAML section of an Rmd document
How about in the YAML:
params:
configuration: NULL
project_conf: NULL
data: NULL
Then in the first chunk something like:
```{r data-config}
if(is.null(params$data)){
data(data_ionstar, package = "prolfqua")
data = data_ionstar
configuration = data$filtered()$config
}
```
You can use a more ornate expression for these parameters when rendering
otherwise `rmarkdown::render()`, which I suppose you could call from a Makefile
if needed when rendering package the vignettes.
Andrew McDavid
Biostatistics and Computational Biology
University of Rochester Medical Center
On Nov 19, 2021, at 6:00 AM,
bioc-devel-requ...@r-project.org wrote:
If anyone wonders, why do I need it. By this I can reuse the vignette
with a different dataset.
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Re: [Bioc-devel] ERROR: More than one VignetteEngine specified.
Hi Witek,
Probably it is a false positive, caused by a commented VignetteEngine on
https://github.com/protViz/prozor/blob/master/vignettes/TargetDecoyFDR_Example.Rmd#L16
If you delete it (and the line below to be sure) I guess it will go away.
Best,
Lluís
On Fri, 19 Nov 2021 at 14:33, Witold Wolski wrote:
> Hi,
>
> I am getting the following error when running BiocCheck
> "ERROR: More than one VignetteEngine specified."
>
> But all the vignettes have the same
> %\VignetteEngine{knitr::rmarkdown}
>
> specified.
> Where else does BiocCheck look for vignetteEngine specification?
>
>
>
> Regards
> Witek
>
> PS. the code can be found here.
> https://github.com/protViz/prozor
>
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>
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[Bioc-devel] ERROR: More than one VignetteEngine specified.
Hi,
I am getting the following error when running BiocCheck
"ERROR: More than one VignetteEngine specified."
But all the vignettes have the same
%\VignetteEngine{knitr::rmarkdown}
specified.
Where else does BiocCheck look for vignetteEngine specification?
Regards
Witek
PS. the code can be found here.
https://github.com/protViz/prozor
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